[ensembl-dev] Is this feature on a patch

[Fairley, Susan]

Hi Jay,

The patch seq_regions are identifiable using seq_region_attrib (the same
mechanism that, for example, identifies toplevel seq_regions).

There are two different attribs - one for novel patches and one for fix
patches.

mysql> select * from attrib_type where attrib_type_id in (312,313);
+----------------+-------------+----------------------+--------------------
---------------------------------------------------------------------------
--------------------------------------------+
| attrib_type_id | code        | name                 | description

                                            |
+----------------+-------------+----------------------+--------------------
---------------------------------------------------------------------------
--------------------------------------------+
|            312 | patch_fix   | Assembly Patch Fix   | Assembly patch
that will, in the next assembly release, replace the corresponding
sequence found in the current assembly                  |
|            313 | patch_novel | Assembly Patch Novel | Assembly patch
that will, in the next assembly release, be retained as an alternate
non-reference sequence in a similar way to haplotypes |
+----------------+-------------+----------------------+--------------------
---------------------------------------------------------------------------
--------------------------------------------+
2 rows in set (0.01 sec)

Checking for those in seq_region_attrib should identify the patches.

Hope that helps,
Susan.



On 30/01/2013 16:21, "Jay Humphrey" <jhumphre at ebi.ac.uk> wrote:

>A little more info:
>The coord systems for these are all name, rank, version = chromosome, 1,
>GRCh37.
>Perhaps one of these (rank?) could be changed in the database without
>impacting other areas?
>
>On 30/01/2013 16:10, Jay Humphrey wrote:
>> In a list of genes and transcripts I want to discard the ones on a
>> patch contig. Is there any way to tell it's a patch besides the name?
>> Examples showing stable id: seq_region_name
>>
>> ENSG00000263007: HG388_HG400_PATCH
>> ENSG00000109846: 11
>> ENST00000574550: HG388_HG400_PATCH
>> ENST00000526180: 11
>>
>
>--
>Jay Humphrey                   Ensembl Genomes Web Developer
>EMBL-EBI                       Tel: +44-(0)1223-492682
>Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
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>
>
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